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- PDB-2o4n: Crystal Structure of HIV-1 Protease (TRM Mutant) in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 2o4n
TitleCrystal Structure of HIV-1 Protease (TRM Mutant) in Complex with Tipranavir
Componentsprotease
KeywordsVIRAL PROTEIN / protease
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / endonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-TPV / Gag-Pol polyprotein / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKang, L.W. / Armstrong, A.A. / Muzammil, S. / Jakalian, A. / Bonneau, P.R. / Schmelmer, V. / Freire, E. / Amzel, L.M.
CitationJournal: J.Virol. / Year: 2007
Title: Unique thermodynamic response of tipranavir to human immunodeficiency virus type 1 protease drug resistance mutations.
Authors: Muzammil, S. / Armstrong, A.A. / Kang, L.W. / Jakalian, A. / Bonneau, P.R. / Schmelmer, V. / Amzel, L.M. / Freire, E.
History
DepositionDec 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protease
B: protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3404
Polymers21,6462
Non-polymers6952
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-26 kcal/mol
Surface area9310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.076, 86.487, 46.439
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein protease /


Mass: 10822.802 Da / Num. of mol.: 2 / Mutation: Q7K, I13V, V32I, L33F, K45I, V82L, I84V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: Subtype B / Gene: gag-pol / Plasmid: pET24 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03367, UniProt: Q90SN9*PLUS
#2: Chemical ChemComp-TPV / N-(3-{(1R)-1-[(6R)-4-HYDROXY-2-OXO-6-PHENETHYL-6-PROPYL-5,6-DIHYDRO-2H-PYRAN-3-YL]PROPYL}PHENYL)-5-(TRIFLUOROMETHYL)-2-PYRIDINESULFONAMIDE / TIPRANAVIR / Tipranavir


Mass: 602.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H33F3N2O5S / Comment: protease inhibitor*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.75-2.0 M NaCl, 100 mM acetate or citrate buffer pH 4.8-5.8 , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 30, 2004 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→19.6 Å / Num. obs: 15839 / % possible obs: 94.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Χ2: 1.142 / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 3.07 / Num. unique all: 1379 / Rsym value: 0.308 / Χ2: 0.846 / % possible all: 84.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.6 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.868 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1587 10.1 %RANDOM
Rwork0.185 ---
obs0.189 15710 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.099 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---1.42 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 2→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 48 191 1759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221598
X-RAY DIFFRACTIONr_angle_refined_deg1.6022.0062169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.795196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.59624.44454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61415282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.593158
X-RAY DIFFRACTIONr_chiral_restr0.1060.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021145
X-RAY DIFFRACTIONr_nbd_refined0.1970.2664
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21065
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2137
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.25
X-RAY DIFFRACTIONr_mcbond_it0.9441.51022
X-RAY DIFFRACTIONr_mcangle_it1.34821586
X-RAY DIFFRACTIONr_scbond_it2.3123672
X-RAY DIFFRACTIONr_scangle_it3.3584.5583
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 86 -
Rwork0.212 865 -
obs-951 97.24 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5424-0.02870.30230.37740.06780.67760.04440.0455-0.0249-0.0342-0.0184-0.00080.04280.0326-0.0260.00460.00340.0029-0.00490.0002-0.031714.837411.50210.3681
20.02870.0330.10250.56670.2850.44110.0117-0.01250.0150.0275-0.011-0.00570.0243-0.0135-0.00080.0031-0.00590.0003-0.00690.0076-0.01616.464522.506228.7604
37.35754.15750.66322.98640.0260.2507-0.0694-0.03850.2153-0.207-0.0410.09360.1698-0.02910.11040.0233-0.0030.0015-0.0038-0.0091-0.024811.481319.246317.6445
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 991 - 99
22BB1 - 991 - 99
33AC300

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